To answer your questions:

1.  Our interrupt handling code always uses specific EOIs.  The npx
    probe is an anomaly, and could easily be changed.

2.  NetBSD doesn't actually program the PIIX3 chip, so I assume this
    is happening in the BIOS.  Can't help you there.

3.  The only reason to use automatic EOIs is that it can be slightly
    faster (by avoiding an extra write to send the EOI to the master
    PIC; it's speced *not* to work on the slave PIC), but on modern
    machines the difference is pretty negligible.  I also found that
    the feature was not reliably implemented, so we don't use it by
    default.